Input reference volume

[Ambroise Desfosses]

Dear Carsten,

when using a reference volume for a refinement (with or without continue option), I tend to use, when available, the latest best map of a previous refinement. I use the output map of Spring (unfiltered, unsymmetrized), without any modification, because I know that the first step will be the symmetrization of this map, and appropriate filtering. However, I am not sure how Spring will deal with the pixel size : can I give any map from any refinement resolution target (LR, MR, HR) as an input, disregarding what resolution target I start with in the new refinement ?

For example, can I give the HR map :

Latest_ref/Latest_ref_2004apix_006.hdf

as an input for a new refinement starting with MR (pixel size 4.008) ? Or should I scale the map first ?

I looked at two reference maps (*_ref_???.hdf) created at the beginning of such a new refinement (but the input reference varied in their pixel size : 2.004 or 4.008). The pixel size written in the header was 1.002 (the un-binned one), as seen by Chimera. But they differed by a factor of 2 when displayed (which would seem logical because one of those refinement was starting at HR and the other at MR).

Am I doing things right ?

Thanks for your help

Best wishes

Ambroise

spring --version && springenv e2version.py 
/programs/x86_64-linux/spring/0.84.1470/bin/python
Spring environment loaded.
GUI from package Emspring-0.84.1470
/programs/x86_64-linux/spring/0.84.1470/bin/python
Spring environment loaded.
EMAN 2.1 alpha2 (CVS 2013/08/07 17:01:09)
Your EMAN2 is running on:  PRETTY_NAME="Debian GNU/Linux 8 (jessie)"
NAME="Debian GNU/Linux"
VERSION_ID="8"
VERSION="8 (jessie)"
ID=debian
HOME_URL="http://www.debian.org/"
SUPPORT_URL="http://www.debian.org/support"
BUG_REPORT_URL="https://bugs.debian.org/" 3.16.0-5-amd64 x86_64
Your Python version is:  2.7.2

[Carsten Sachse]

Dear Ambroise,

Thank you for your question. If the reference volume has been generated in SPRING. SPRING will recognize the pixel size information in the header and interpolate as needed to bring it back to the original pixel size.

See my response below.

On Tuesday, 13 March 2018 10:59:05 UTC+1, Ambroise Desfosses wrote:

Dear Carsten,

when using a reference volume for a refinement (with or without continue option), I tend to use, when available, the latest best map of a previous refinement. I use the output map of Spring (unfiltered, unsymmetrized), without any modification, because I know that the first step will be the symmetrization of this map, and appropriate filtering. However, I am not sure how Spring will deal with the pixel size : can I give any map from any refinement resolution target (LR, MR, HR) as an input, disregarding what resolution target I start with in the new refinement ?

SPRING will recognize the pixel size information in the header and deal with it appropriately.

 

For example, can I give the HR map :
Latest_ref/Latest_ref_2004apix_006.hdf

as an input for a new refinement starting with MR (pixel size 4.008) ? Or should I scale the map first ?

No scaling is required as SPRING will take care of it. 

I looked at two reference maps (*_ref_???.hdf) created at the beginning of such a new refinement (but the input reference varied in their pixel size : 2.004 or 4.008). The pixel size written in the header was 1.002 (the un-binned one), as seen by Chimera. But they differed by a factor of 2 when displayed (which would seem logical because one of those refinement was starting at HR and the other at MR).

Am I doing things right ?

This observation is correct as SPRING prepares the reference for the pixel size to be run within target resolution regime to be refined (low resolution, medium resolution, high resolution and max resolution).

I hope this explains the issue.

Best wishes,

Carsten 

[Ambroise Desfosses]

Dear Carsten,
yes it does answer the question, thanks.
Ambroise